diff --git a/doc/filters.texi b/doc/filters.texi
index 57189c77b0..690a60f569 100644
--- a/doc/filters.texi
+++ b/doc/filters.texi
@@ -11531,6 +11531,13 @@ The option must be an integer value in the range [0,5]. Default is @var{2}.
 @item diff_mode
 If set, define the zone to process
 
+@item threshold
+Sets the alpha threshold for transparency. Alpha values above this threshold
+will be treated as completely opaque, and values below this threshold will be
+treated as completely transparent.
+
+The option must be an integer value in the range [0,255]. Default is 128.
+
 @table @samp
 @item rectangle
 Only the changing rectangle will be reprocessed. This is similar to GIF
diff --git a/libavfilter/vf_paletteuse.c b/libavfilter/vf_paletteuse.c
index 79a0672891..40ec3b2a78 100644
--- a/libavfilter/vf_paletteuse.c
+++ b/libavfilter/vf_paletteuse.c
@@ -56,7 +56,7 @@ enum diff_mode {
 };
 
 struct color_node {
-    uint8_t val[3];
+    uint8_t val[4];
     uint8_t palette_id;
     int split;
     int left_id, right_id;
@@ -86,6 +86,8 @@ typedef struct PaletteUseContext {
     struct cache_node cache[CACHE_SIZE];    /* lookup cache */
     struct color_node map[AVPALETTE_COUNT]; /* 3D-Tree (KD-Tree with K=3) for reverse colormap */
     uint32_t palette[AVPALETTE_COUNT];
+    int transparency_index; /* index in the palette of transparency. -1 if there is no transparency in the palette. */
+    int trans_thresh;
     int palette_loaded;
     int dither;
     int new;
@@ -116,6 +118,7 @@ static const AVOption paletteuse_options[] = {
     { "bayer_scale", "set scale for bayer dithering", OFFSET(bayer_scale), AV_OPT_TYPE_INT, {.i64=2}, 0, 5, FLAGS },
     { "diff_mode",   "set frame difference mode",     OFFSET(diff_mode),   AV_OPT_TYPE_INT, {.i64=DIFF_MODE_NONE}, 0, NB_DIFF_MODE-1, FLAGS, "diff_mode" },
         { "rectangle", "process smallest different rectangle", 0, AV_OPT_TYPE_CONST, {.i64=DIFF_MODE_RECTANGLE}, INT_MIN, INT_MAX, FLAGS, "diff_mode" },
+    { "threshold", "set the alpha threshold for transparency.", OFFSET(trans_thresh), AV_OPT_TYPE_INT, {.i64=128}, 0, 255, },
 
     /* following are the debug options, not part of the official API */
     { "debug_kdtree", "save Graphviz graph of the kdtree in specified file", OFFSET(dot_filename), AV_OPT_TYPE_STRING, {.str=NULL}, CHAR_MIN, CHAR_MAX, FLAGS },
@@ -157,34 +160,43 @@ static int query_formats(AVFilterContext *ctx)
 
 static av_always_inline int dither_color(uint32_t px, int er, int eg, int eb, int scale, int shift)
 {
-    return av_clip_uint8((px >> 16 & 0xff) + ((er * scale) / (1<<shift))) << 16
+    return av_clip_uint8( px >> 24                                      ) << 24
+         | av_clip_uint8((px >> 16 & 0xff) + ((er * scale) / (1<<shift))) << 16
          | av_clip_uint8((px >>  8 & 0xff) + ((eg * scale) / (1<<shift))) <<  8
          | av_clip_uint8((px       & 0xff) + ((eb * scale) / (1<<shift)));
 }
 
-static av_always_inline int diff(const uint8_t *c1, const uint8_t *c2)
+static av_always_inline int diff(const uint8_t *c1, const uint8_t *c2, const int trans_thresh)
 {
     // XXX: try L*a*b with CIE76 (dL*dL + da*da + db*db)
-    const int dr = c1[0] - c2[0];
-    const int dg = c1[1] - c2[1];
-    const int db = c1[2] - c2[2];
-    return dr*dr + dg*dg + db*db;
+    const int dr = c1[1] - c2[1];
+    const int dg = c1[2] - c2[2];
+    const int db = c1[3] - c2[3];
+
+    if (c1[0] < trans_thresh && c2[0] < trans_thresh) {
+        return 0;
+    } else if (c1[0] >= trans_thresh && c2[0] >= trans_thresh) {
+        return dr*dr + dg*dg + db*db;
+    } else {
+        return 255*255 + 255*255 + 255*255;
+    }
 }
 
-static av_always_inline uint8_t colormap_nearest_bruteforce(const uint32_t *palette, const uint8_t *rgb)
+static av_always_inline uint8_t colormap_nearest_bruteforce(const uint32_t *palette, const uint8_t *argb, const int trans_thresh)
 {
     int i, pal_id = -1, min_dist = INT_MAX;
 
     for (i = 0; i < AVPALETTE_COUNT; i++) {
         const uint32_t c = palette[i];
 
-        if ((c & 0xff000000) == 0xff000000) { // ignore transparent entry
-            const uint8_t palrgb[] = {
+        if ( c >> 24 >= trans_thresh ) { // ignore transparent entry
+            const uint8_t palargb[] = {
+                palette[i]>>24 & 0xff,
                 palette[i]>>16 & 0xff,
                 palette[i]>> 8 & 0xff,
                 palette[i]     & 0xff,
             };
-            const int d = diff(palrgb, rgb);
+            const int d = diff(palargb, argb, trans_thresh);
             if (d < min_dist) {
                 pal_id = i;
                 min_dist = d;
@@ -203,13 +215,14 @@ struct nearest_color {
 static void colormap_nearest_node(const struct color_node *map,
                                   const int node_pos,
                                   const uint8_t *target,
+                                  const int trans_thresh,
                                   struct nearest_color *nearest)
 {
     const struct color_node *kd = map + node_pos;
     const int s = kd->split;
     int dx, nearer_kd_id, further_kd_id;
     const uint8_t *current = kd->val;
-    const int current_to_target = diff(target, current);
+    const int current_to_target = diff(target, current, trans_thresh);
 
     if (current_to_target < nearest->dist_sqd) {
         nearest->node_pos = node_pos;
@@ -223,17 +236,17 @@ static void colormap_nearest_node(const struct color_node *map,
         else         nearer_kd_id = kd->right_id, further_kd_id = kd->left_id;
 
         if (nearer_kd_id != -1)
-            colormap_nearest_node(map, nearer_kd_id, target, nearest);
+            colormap_nearest_node(map, nearer_kd_id, target, trans_thresh, nearest);
 
         if (further_kd_id != -1 && dx*dx < nearest->dist_sqd)
-            colormap_nearest_node(map, further_kd_id, target, nearest);
+            colormap_nearest_node(map, further_kd_id, target, trans_thresh, nearest);
     }
 }
 
-static av_always_inline uint8_t colormap_nearest_recursive(const struct color_node *node, const uint8_t *rgb)
+static av_always_inline uint8_t colormap_nearest_recursive(const struct color_node *node, const uint8_t *rgb, const int trans_thresh)
 {
     struct nearest_color res = {.dist_sqd = INT_MAX, .node_pos = -1};
-    colormap_nearest_node(node, 0, rgb, &res);
+    colormap_nearest_node(node, 0, rgb, trans_thresh, &res);
     return node[res.node_pos].palette_id;
 }
 
@@ -242,7 +255,7 @@ struct stack_node {
     int dx2;
 };
 
-static av_always_inline uint8_t colormap_nearest_iterative(const struct color_node *root, const uint8_t *target)
+static av_always_inline uint8_t colormap_nearest_iterative(const struct color_node *root, const uint8_t *target, const int trans_thresh)
 {
     int pos = 0, best_node_id = -1, best_dist = INT_MAX, cur_color_id = 0;
     struct stack_node nodes[16];
@@ -252,7 +265,7 @@ static av_always_inline uint8_t colormap_nearest_iterative(const struct color_no
 
         const struct color_node *kd = &root[cur_color_id];
         const uint8_t *current = kd->val;
-        const int current_to_target = diff(target, current);
+        const int current_to_target = diff(target, current, trans_thresh);
 
         /* Compare current color node to the target and update our best node if
          * it's actually better. */
@@ -314,25 +327,27 @@ end:
     return root[best_node_id].palette_id;
 }
 
-#define COLORMAP_NEAREST(search, palette, root, target)                                    \
-    search == COLOR_SEARCH_NNS_ITERATIVE ? colormap_nearest_iterative(root, target) :      \
-    search == COLOR_SEARCH_NNS_RECURSIVE ? colormap_nearest_recursive(root, target) :      \
-                                           colormap_nearest_bruteforce(palette, target)
+#define COLORMAP_NEAREST(search, palette, root, target, trans_thresh)                                    \
+    search == COLOR_SEARCH_NNS_ITERATIVE ? colormap_nearest_iterative(root, target, trans_thresh) :      \
+    search == COLOR_SEARCH_NNS_RECURSIVE ? colormap_nearest_recursive(root, target, trans_thresh) :      \
+                                           colormap_nearest_bruteforce(palette, target, trans_thresh)
 
 /**
  * Check if the requested color is in the cache already. If not, find it in the
  * color tree and cache it.
- * Note: r, g, and b are the component of c but are passed as well to avoid
+ * Note: a, r, g, and b are the components of color, but are passed as well to avoid
  * recomputing them (they are generally computed by the caller for other uses).
  */
 static av_always_inline int color_get(struct cache_node *cache, uint32_t color,
-                                      uint8_t r, uint8_t g, uint8_t b,
+                                      uint8_t a, uint8_t r, uint8_t g, uint8_t b,
+                                      int transparency_index,
+                                      int trans_thresh,
                                       const struct color_node *map,
                                       const uint32_t *palette,
                                       const enum color_search_method search_method)
 {
     int i;
-    const uint8_t rgb[] = {r, g, b};
+    const uint8_t argb_elts[] = {a, r, g, b};
     const uint8_t rhash = r & ((1<<NBITS)-1);
     const uint8_t ghash = g & ((1<<NBITS)-1);
     const uint8_t bhash = b & ((1<<NBITS)-1);
@@ -340,6 +355,11 @@ static av_always_inline int color_get(struct cache_node *cache, uint32_t color,
     struct cache_node *node = &cache[hash];
     struct cached_color *e;
 
+    // first, check for transparency
+    if (a < trans_thresh && transparency_index >= 0) {
+        return transparency_index;
+    }
+
     for (i = 0; i < node->nb_entries; i++) {
         e = &node->entries[i];
         if (e->color == color)
@@ -351,20 +371,24 @@ static av_always_inline int color_get(struct cache_node *cache, uint32_t color,
     if (!e)
         return AVERROR(ENOMEM);
     e->color = color;
-    e->pal_entry = COLORMAP_NEAREST(search_method, palette, map, rgb);
+    e->pal_entry = COLORMAP_NEAREST(search_method, palette, map, argb_elts, trans_thresh);
+
     return e->pal_entry;
 }
 
 static av_always_inline int get_dst_color_err(struct cache_node *cache,
                                               uint32_t c, const struct color_node *map,
                                               const uint32_t *palette,
+                                              int transparency_index,
+                                              int trans_thresh,
                                               int *er, int *eg, int *eb,
                                               const enum color_search_method search_method)
 {
+    const uint8_t a = c >> 24 & 0xff;
     const uint8_t r = c >> 16 & 0xff;
     const uint8_t g = c >>  8 & 0xff;
     const uint8_t b = c       & 0xff;
-    const int dstx = color_get(cache, c, r, g, b, map, palette, search_method);
+    const int dstx = color_get(cache, c, a, r, g, b, transparency_index, trans_thresh, map, palette, search_method);
     const uint32_t dstc = palette[dstx];
     *er = r - (dstc >> 16 & 0xff);
     *eg = g - (dstc >>  8 & 0xff);
@@ -385,6 +409,8 @@ static av_always_inline int set_frame(PaletteUseContext *s, AVFrame *out, AVFram
     const int dst_linesize = out->linesize[0];
     uint32_t *src = ((uint32_t *)in ->data[0]) + y_start*src_linesize;
     uint8_t  *dst =              out->data[0]  + y_start*dst_linesize;
+    int transparency_index = s->transparency_index;
+    int trans_thresh = s->trans_thresh;
 
     w += x_start;
     h += y_start;
@@ -395,14 +421,14 @@ static av_always_inline int set_frame(PaletteUseContext *s, AVFrame *out, AVFram
 
             if (dither == DITHERING_BAYER) {
                 const int d = s->ordered_dither[(y & 7)<<3 | (x & 7)];
+                const uint8_t a8 = src[x] >> 24 & 0xff;
                 const uint8_t r8 = src[x] >> 16 & 0xff;
                 const uint8_t g8 = src[x] >>  8 & 0xff;
                 const uint8_t b8 = src[x]       & 0xff;
                 const uint8_t r = av_clip_uint8(r8 + d);
                 const uint8_t g = av_clip_uint8(g8 + d);
                 const uint8_t b = av_clip_uint8(b8 + d);
-                const uint32_t c = r<<16 | g<<8 | b;
-                const int color = color_get(cache, c, r, g, b, map, palette, search_method);
+                const int color = color_get(cache, src[x], a8, r, g, b, transparency_index, trans_thresh, map, palette, search_method);
 
                 if (color < 0)
                     return color;
@@ -410,7 +436,7 @@ static av_always_inline int set_frame(PaletteUseContext *s, AVFrame *out, AVFram
 
             } else if (dither == DITHERING_HECKBERT) {
                 const int right = x < w - 1, down = y < h - 1;
-                const int color = get_dst_color_err(cache, src[x], map, palette, &er, &eg, &eb, search_method);
+                const int color = get_dst_color_err(cache, src[x], map, palette, transparency_index, trans_thresh, &er, &eg, &eb, search_method);
 
                 if (color < 0)
                     return color;
@@ -422,7 +448,7 @@ static av_always_inline int set_frame(PaletteUseContext *s, AVFrame *out, AVFram
 
             } else if (dither == DITHERING_FLOYD_STEINBERG) {
                 const int right = x < w - 1, down = y < h - 1, left = x > x_start;
-                const int color = get_dst_color_err(cache, src[x], map, palette, &er, &eg, &eb, search_method);
+                const int color = get_dst_color_err(cache, src[x], map, palette, transparency_index, trans_thresh, &er, &eg, &eb, search_method);
 
                 if (color < 0)
                     return color;
@@ -436,7 +462,7 @@ static av_always_inline int set_frame(PaletteUseContext *s, AVFrame *out, AVFram
             } else if (dither == DITHERING_SIERRA2) {
                 const int right  = x < w - 1, down  = y < h - 1, left  = x > x_start;
                 const int right2 = x < w - 2,                    left2 = x > x_start + 1;
-                const int color = get_dst_color_err(cache, src[x], map, palette, &er, &eg, &eb, search_method);
+                const int color = get_dst_color_err(cache, src[x], map, palette, transparency_index, trans_thresh, &er, &eg, &eb, search_method);
 
                 if (color < 0)
                     return color;
@@ -455,7 +481,7 @@ static av_always_inline int set_frame(PaletteUseContext *s, AVFrame *out, AVFram
 
             } else if (dither == DITHERING_SIERRA2_4A) {
                 const int right = x < w - 1, down = y < h - 1, left = x > x_start;
-                const int color = get_dst_color_err(cache, src[x], map, palette, &er, &eg, &eb, search_method);
+                const int color = get_dst_color_err(cache, src[x], map, palette, transparency_index, trans_thresh, &er, &eg, &eb, search_method);
 
                 if (color < 0)
                     return color;
@@ -466,10 +492,11 @@ static av_always_inline int set_frame(PaletteUseContext *s, AVFrame *out, AVFram
                 if (         down) src[src_linesize + x    ] = dither_color(src[src_linesize + x    ], er, eg, eb, 1, 2);
 
             } else {
+                const uint8_t a = src[x] >> 24 & 0xff;
                 const uint8_t r = src[x] >> 16 & 0xff;
                 const uint8_t g = src[x] >>  8 & 0xff;
                 const uint8_t b = src[x]       & 0xff;
-                const int color = color_get(cache, src[x] & 0xffffff, r, g, b, map, palette, search_method);
+                const int color = color_get(cache, src[x], a, r, g, b, transparency_index, trans_thresh, map, palette, search_method);
 
                 if (color < 0)
                     return color;
@@ -489,19 +516,19 @@ static void disp_node(AVBPrint *buf,
                       int depth)
 {
     const struct color_node *node = &map[node_id];
-    const uint32_t fontcolor = node->val[0] > 0x50 &&
-                               node->val[1] > 0x50 &&
-                               node->val[2] > 0x50 ? 0 : 0xffffff;
+    const uint32_t fontcolor = node->val[1] > 0x50 &&
+                               node->val[2] > 0x50 &&
+                               node->val[3] > 0x50 ? 0 : 0xffffff;
     av_bprintf(buf, "%*cnode%d ["
                "label=\"%c%02X%c%02X%c%02X%c\" "
                "fillcolor=\"#%02x%02x%02x\" "
                "fontcolor=\"#%06"PRIX32"\"]\n",
                depth*INDENT, ' ', node->palette_id,
-               "[  "[node->split], node->val[0],
-               "][ "[node->split], node->val[1],
-               " ]["[node->split], node->val[2],
+               "[  "[node->split], node->val[1],
+               "][ "[node->split], node->val[2],
+               " ]["[node->split], node->val[3],
                "  ]"[node->split],
-               node->val[0], node->val[1], node->val[2],
+               node->val[1], node->val[2], node->val[3],
                fontcolor);
     if (parent_id != -1)
         av_bprintf(buf, "%*cnode%d -> node%d\n", depth*INDENT, ' ',
@@ -536,7 +563,7 @@ static int disp_tree(const struct color_node *node, const char *fname)
     return 0;
 }
 
-static int debug_accuracy(const struct color_node *node, const uint32_t *palette,
+static int debug_accuracy(const struct color_node *node, const uint32_t *palette, const int trans_thresh,
                           const enum color_search_method search_method)
 {
     int r, g, b, ret = 0;
@@ -545,15 +572,15 @@ static int debug_accuracy(const struct color_node *node, const uint32_t *palette
         for (g = 0; g < 256; g++) {
             for (b = 0; b < 256; b++) {
                 const uint8_t rgb[] = {r, g, b};
-                const int r1 = COLORMAP_NEAREST(search_method, palette, node, rgb);
-                const int r2 = colormap_nearest_bruteforce(palette, rgb);
+                const int r1 = COLORMAP_NEAREST(search_method, palette, node, rgb, trans_thresh);
+                const int r2 = colormap_nearest_bruteforce(palette, rgb, trans_thresh);
                 if (r1 != r2) {
                     const uint32_t c1 = palette[r1];
                     const uint32_t c2 = palette[r2];
                     const uint8_t palrgb1[] = { c1>>16 & 0xff, c1>> 8 & 0xff, c1 & 0xff };
                     const uint8_t palrgb2[] = { c2>>16 & 0xff, c2>> 8 & 0xff, c2 & 0xff };
-                    const int d1 = diff(palrgb1, rgb);
-                    const int d2 = diff(palrgb2, rgb);
+                    const int d1 = diff(palrgb1, rgb, trans_thresh);
+                    const int d2 = diff(palrgb2, rgb, trans_thresh);
                     if (d1 != d2) {
                         av_log(NULL, AV_LOG_ERROR,
                                "/!\\ %02X%02X%02X: %d ! %d (%06"PRIX32" ! %06"PRIX32") / dist: %d ! %d\n",
@@ -584,17 +611,19 @@ static int cmp_##name(const void *pa, const void *pb)   \
 {                                                       \
     const struct color *a = pa;                         \
     const struct color *b = pb;                         \
-    return   (a->value >> (8 * (2 - (pos))) & 0xff)     \
-           - (b->value >> (8 * (2 - (pos))) & 0xff);    \
+    return   (a->value >> (8 * (3 - (pos))) & 0xff)     \
+           - (b->value >> (8 * (3 - (pos))) & 0xff);    \
 }
 
-DECLARE_CMP_FUNC(r, 0)
-DECLARE_CMP_FUNC(g, 1)
-DECLARE_CMP_FUNC(b, 2)
+DECLARE_CMP_FUNC(a, 0)
+DECLARE_CMP_FUNC(r, 1)
+DECLARE_CMP_FUNC(g, 2)
+DECLARE_CMP_FUNC(b, 3)
 
-static const cmp_func cmp_funcs[] = {cmp_r, cmp_g, cmp_b};
+static const cmp_func cmp_funcs[] = {cmp_a, cmp_r, cmp_g, cmp_b};
 
 static int get_next_color(const uint8_t *color_used, const uint32_t *palette,
+                          const int trans_thresh,
                           int *component, const struct color_rect *box)
 {
     int wr, wg, wb;
@@ -609,11 +638,16 @@ static int get_next_color(const uint8_t *color_used, const uint32_t *palette,
 
     for (i = 0; i < AVPALETTE_COUNT; i++) {
         const uint32_t c = palette[i];
+        const uint8_t a = c >> 24 & 0xff;
         const uint8_t r = c >> 16 & 0xff;
         const uint8_t g = c >>  8 & 0xff;
         const uint8_t b = c       & 0xff;
 
-        if (color_used[i] ||
+        if (a < trans_thresh) {
+            continue;
+        }
+
+        if (color_used[i] || (a != 0xff) ||
             r < box->min[0] || g < box->min[1] || b < box->min[2] ||
             r > box->max[0] || g > box->max[1] || b > box->max[2])
             continue;
@@ -639,9 +673,9 @@ static int get_next_color(const uint8_t *color_used, const uint32_t *palette,
     wr = ranges.max[0] - ranges.min[0];
     wg = ranges.max[1] - ranges.min[1];
     wb = ranges.max[2] - ranges.min[2];
-    if (wr >= wg && wr >= wb) longest = 0;
-    if (wg >= wr && wg >= wb) longest = 1;
-    if (wb >= wr && wb >= wg) longest = 2;
+    if (wr >= wg && wr >= wb) longest = 1;
+    if (wg >= wr && wg >= wb) longest = 2;
+    if (wb >= wr && wb >= wg) longest = 3;
     cmpf = cmp_funcs[longest];
     *component = longest;
 
@@ -655,6 +689,7 @@ static int colormap_insert(struct color_node *map,
                            uint8_t *color_used,
                            int *nb_used,
                            const uint32_t *palette,
+                           const int trans_thresh,
                            const struct color_rect *box)
 {
     uint32_t c;
@@ -662,7 +697,7 @@ static int colormap_insert(struct color_node *map,
     int node_left_id = -1, node_right_id = -1;
     struct color_node *node;
     struct color_rect box1, box2;
-    const int pal_id = get_next_color(color_used, palette, &component, box);
+    const int pal_id = get_next_color(color_used, palette, trans_thresh, &component, box);
 
     if (pal_id < 0)
         return -1;
@@ -673,21 +708,22 @@ static int colormap_insert(struct color_node *map,
     node = &map[cur_id];
     node->split = component;
     node->palette_id = pal_id;
-    node->val[0] = c>>16 & 0xff;
-    node->val[1] = c>> 8 & 0xff;
-    node->val[2] = c     & 0xff;
+    node->val[0] = c>>24 & 0xff;
+    node->val[1] = c>>16 & 0xff;
+    node->val[2] = c>> 8 & 0xff;
+    node->val[3] = c     & 0xff;
 
     color_used[pal_id] = 1;
 
     /* get the two boxes this node creates */
     box1 = box2 = *box;
-    box1.max[component] = node->val[component];
-    box2.min[component] = node->val[component] + 1;
+    box1.max[component-1] = node->val[component];
+    box2.min[component-1] = node->val[component] + 1;
 
-    node_left_id = colormap_insert(map, color_used, nb_used, palette, &box1);
+    node_left_id = colormap_insert(map, color_used, nb_used, palette, trans_thresh, &box1);
 
-    if (box2.min[component] <= box2.max[component])
-        node_right_id = colormap_insert(map, color_used, nb_used, palette, &box2);
+    if (box2.min[component-1] <= box2.max[component-1])
+        node_right_id = colormap_insert(map, color_used, nb_used, palette, trans_thresh, &box2);
 
     node->left_id  = node_left_id;
     node->right_id = node_right_id;
@@ -711,6 +747,16 @@ static void load_colormap(PaletteUseContext *s)
 
     /* disable transparent colors and dups */
     qsort(s->palette, AVPALETTE_COUNT, sizeof(*s->palette), cmp_pal_entry);
+    // update transparency index:
+    if (s->transparency_index >= 0) {
+        for (i = 0; i < AVPALETTE_COUNT; i++) {
+            if ((s->palette[i]>>24 & 0xff) == 0) {
+                s->transparency_index = i; // we are assuming at most one transparent color in palette
+                break;
+            }
+        }
+    }
+
     for (i = 0; i < AVPALETTE_COUNT; i++) {
         const uint32_t c = s->palette[i];
         if (i != 0 && c == last_color) {
@@ -718,7 +764,7 @@ static void load_colormap(PaletteUseContext *s)
             continue;
         }
         last_color = c;
-        if ((c & 0xff000000) != 0xff000000) {
+        if (c >> 24 < s->trans_thresh) {
             color_used[i] = 1; // ignore transparent color(s)
             continue;
         }
@@ -727,13 +773,13 @@ static void load_colormap(PaletteUseContext *s)
     box.min[0] = box.min[1] = box.min[2] = 0x00;
     box.max[0] = box.max[1] = box.max[2] = 0xff;
 
-    colormap_insert(s->map, color_used, &nb_used, s->palette, &box);
+    colormap_insert(s->map, color_used, &nb_used, s->palette, s->trans_thresh, &box);
 
     if (s->dot_filename)
         disp_tree(s->map, s->dot_filename);
 
     if (s->debug_accuracy) {
-        if (!debug_accuracy(s->map, s->palette, s->color_search_method))
+        if (!debug_accuracy(s->map, s->palette, s->trans_thresh, s->color_search_method))
             av_log(NULL, AV_LOG_INFO, "Accuracy check passed\n");
     }
 }
@@ -756,7 +802,7 @@ static void debug_mean_error(PaletteUseContext *s, const AVFrame *in1,
             const uint32_t c2 = palette[src2[x]];
             const uint8_t rgb1[] = {c1 >> 16 & 0xff, c1 >> 8 & 0xff, c1 & 0xff};
             const uint8_t rgb2[] = {c2 >> 16 & 0xff, c2 >> 8 & 0xff, c2 & 0xff};
-            mean_err += diff(rgb1, rgb2);
+            mean_err += diff(rgb1, rgb2, s->trans_thresh);
         }
         src1 += src1_linesize;
         src2 += src2_linesize;
@@ -941,6 +987,8 @@ static void load_palette(PaletteUseContext *s, const AVFrame *palette_frame)
     const uint32_t *p = (const uint32_t *)palette_frame->data[0];
     const int p_linesize = palette_frame->linesize[0] >> 2;
 
+    s->transparency_index = -1;
+
     if (s->new) {
         memset(s->palette, 0, sizeof(s->palette));
         memset(s->map, 0, sizeof(s->map));
@@ -951,8 +999,13 @@ static void load_palette(PaletteUseContext *s, const AVFrame *palette_frame)
 
     i = 0;
     for (y = 0; y < palette_frame->height; y++) {
-        for (x = 0; x < palette_frame->width; x++)
-            s->palette[i++] = p[x];
+        for (x = 0; x < palette_frame->width; x++) {
+            s->palette[i] = p[x];
+            if (p[x]>>24 < s->trans_thresh) {
+                s->transparency_index = i; // we are assuming at most one transparent color in palette
+            }
+            i++;
+        }
         p += p_linesize;
     }
 
